Marine sponges often contain diverse and abundant communities of microorganisms including bacteria, archaea and eukaryotic microbes. Numerous 16S rRNA-based studies have identified putative 'sponge-specific' microbes that are apparently absent from seawater and other (non-sponge) marine habitats. With more than 7500 sponge-derived rRNA sequences (from clone, isolate and denaturing gradient gel electrophoresis data) now publicly available, we sought to determine whether the current notion of sponge-specific sequence clusters remains valid. Comprehensive phylogenetic analyses were performed on the 7546 sponge-derived 16S and 18S rRNA sequences that were publicly available in early 2010. Overall, 27% of all sequences fell into monophyletic, sponge-specific sequence clusters. Such clusters were particularly well represented among the Chloroflexi, Cyanobacteria, 'Poribacteria', Betaproteobacteria and Acidobacteria, and in total were identified in at least 14 bacterial phyla, as well as the Archaea and fungi. The largest sponge-specific cluster, representing the cyanobacterium 'Synechococcus spongiarum', contained 245 sequences from 40 sponge species. These results strongly support the existence of sponge-specific microbes and provide a suitable framework for future studies of rare and abundant sponge symbionts, both of which can now be studied using next-generation sequencing technologies.

Atmospheric carbon dioxide (CO2) levels are rapidly rising causing an increase in the partial pressure of CO2 (pCO2) in the ocean and a reduction in pH known as ocean acidification (OA). Natural volcanic seeps in Papua New Guinea expel 99% pure CO2 and thereby offer a unique opportunity to explore the effects of OA in situ. The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO2 seep than at nearby control sites <500 m away. A primary driver of microbial differences in A. millepora was a 50% reduction of symbiotic Endozoicomonas. This loss of symbiotic taxa from corals at the CO2 seep highlights a potential hurdle for corals to overcome if they are to adapt to and survive OA. In contrast, the two sponges Coelocarteria singaporensis and Cinachyra sp. were ∼40-fold more abundant at the seep and hosted a significantly higher relative abundance of Synechococcus than sponges at control sites. The increase in photosynthetic microbes at the seep potentially provides these species with a nutritional benefit and enhanced scope for growth under future climate scenarios (thus, flexibility in symbiosis may lead to a larger niche breadth). The microbial community in the apparently pCO2-sensitive sponge species S. massa was not significantly different between sites. These data show that responses to elevated pCO2 are species-specific and that the stability and flexibility of microbial partnerships may have an important role in shaping and contributing to the fitness and success of some hosts.

Numerous studies have reported the existence of sponge-specific 16S ribosomal RNA (rRNA) gene sequence clusters, representing bacteria found in sponges but not detected in other environments, such as seawater. The advent of deep-sequencing technologies allows us to examine the rare microbial biosphere in order to establish whether these bacteria are truly sponge specific, or are more widely distributed but only at abundances below the detection limit of conventional molecular approaches. We screened 412 million publicly available 16S rRNA gene pyrotags derived from 649 seawater, sediment, hydrothermal vent and coral samples from temperate, tropical and polar regions. We detected 77 of the 173 previously described sponge-specific clusters in seawater or other non-sponge samples, albeit generally at extremely low abundances. Sequences representing the candidate phylum 'Poribacteria', previously thought to be largely restricted to sponges, were recovered from 46 (out of 411) seawater and 41 (out of 129) sediment samples. While the presence of an organism does not imply that it is active in situ, our results do suggest that many 'spongespecific' bacteria occur more widely outside of sponge hosts than previously thought. The ISME Journal (2013) 7, 438-443; doi:10.1038/ismej.2012.111; published online 4 October 2012Subject Category: microbe-microbe and microbe-host interactions Keywords: marine sponge; bacteria; specificity; 16S rRNA pyrosequencing Marine sponges form relationships with a diverse range of microbes (Taylor et al., 2007;Webster and Taylor, 2012), and many of these associations are highly host specific (Schmitt et al., 2012). Numerous studies have reported the existence of monophyletic sponge-specific 16S ribosomal RNA (rRNA) gene sequence clusters, representing bacteria found in sponges but not detected in other environments, such as seawater (Hentschel et al., 2002;Taylor et al., 2007;Simister et al., 2012). In a recent 16S rRNA gene tag pyrosequencing study (Webster et al., 2010), we revealed the presence of sequences affiliated with 'sponge-specific' clusters in seawater. While this finding suggests that 'sponge-specific' bacteria can in fact reside outside of these hosts, the seawater was collected only 10 m away from the sampled sponges at the time of sponge spawning and thus a sponge origin for these bacteria could not be unequivocally ruled out. To clarify this fundamental issue in sponge symbiont biology, we examined 412 million 16S rRNA gene pyrotags (V6 region) generated under the auspices of the International Census of Marine Microbes (ICoMM; http://icomm.mbl.edu/). These sequences were derived from a range of seawater, sediment, hydrothermal vent and coral samples obtained from temperate, tropical and polar regions (Figure 1). The absence of 'sponge-specific' bacteria from these samples would provide strong additional evidence for their host specificity, whereas their widespread occurrence among non-sponge samples would imply that they are capable of at least surviving in a free-living state...

Key calcifying reef taxa are currently threatened by thermal stress associated with elevated sea surface temperatures (SST) and reduced calcification linked to ocean acidification (OA). Here we undertook an 8 week experimental exposure to near-future climate change conditions and explored the microbiome response of the corals Acropora millepora and Seriatopora hystrix, the crustose coralline algae Hydrolithon onkodes, the foraminifera Marginopora vertebralis and Heterostegina depressa and the sea urchin Echinometra sp. Microbial communities of all taxa were tolerant of elevated pCO2/reduced pH, exhibiting stable microbial communities between pH 8.1 (pCO2 479–499 μatm) and pH 7.9 (pCO2 738–835 μatm). In contrast, microbial communities of the CCA and foraminifera were sensitive to elevated seawater temperature, with a significant microbial shift involving loss of specific taxa and appearance of novel microbial groups occurring between 28 and 31 °C. An interactive effect between stressors was also identified, with distinct communities developing under different pCO2 conditions only evident at 31 °C. Microbiome analysis of key calcifying coral reef species under near-future climate conditions highlights the importance of assessing impacts from both increased SST and OA, as combinations of these global stressors can amplify microbial shifts which may have concomitant impacts for coral reef structure and function.

Crustose coralline algae (CCA) are a critical component of coral reefs as they accrete carbonate for reef structure and act as settlement substrata for many invertebrates including corals. CCA host a diversity of microorganisms that can also play a role in coral settlement and metamorphosis processes. Although the sensitivity of CCA to ocean acidification (OA) is well established, the response of their associated microbial communities to reduced pH and increased CO2 was previously not known. Here we investigate the sensitivity of CCA-associated microbial biofilms to OA and determine whether or not OA adversely affects the ability of CCA to induce coral larval metamorphosis. We experimentally exposed the CCA Hydrolithon onkodes to four pH/pCO2 conditions consistent with current IPCC predictions for the next few centuries (pH: 8.1, 7.9, 7.7, 7.5, pCO2: 464, 822, 1187, 1638 μatm). Settlement and metamorphosis of coral larvae was reduced on CCA pre-exposed to pH 7.7 (pCO2 = 1187 μatm) and below over a 6-week period. Additional experiments demonstrated that low pH treatments did not directly affect the ability of larvae to settle, but instead most likely altered the biochemistry of the CCA or its microbial associates. Detailed microbial community analysis of the CCA revealed diverse bacterial assemblages that altered significantly between pH 8.1 (pCO2 = 464 μatm) and pH 7.9 (pCO2 = 822 μatm) with this trend continuing at lower pH/higher pCO2 treatments. The shift in microbial community composition primarily comprised changes in the abundance of the dominant microbes between the different pH treatments and the appearance of new (but rare) microbes at pH 7.5. Microbial shifts and the concomitant reduced ability of CCA to induce coral settlement under OA conditions projected to occur by 2100 is a significant concern for the development, maintenance and recovery of reefs globally.